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Electron microscopy / Image analysis / 3D reconstruction

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Read out file names of a folder (Mac & PC)

Posted on 8. June 201919. November 2022by Stefan

In order to be able to quickly put together multiple file names for a .txt import of images for TrakEM2 (without typing all file names) for example, the two following processes can be used. On a Mac: mark all files in the folder, right click & copy and paste it to a .txt file or […]

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About me

Hi, I am Stefan Fischer. I am biologist at the University of Tübingen and Head of Tübingen Structural Microscopy Core Facility (TSM). My methodological interest is set on electron microscopy. Furthermore I do focus on 3D techniques, be it on basis of semi-thin sections (LM), Ultra-thin sections (ssTEM) and also MicroCT data. For that reason I developed a strong interest in open source software packages and image analysis in order to automate (or semi-automate) some of the tedious parts of my workflows.

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alignment Amira Arithmetic tool commandline exchange export Fiji Import Label macro memory MicroCT preprocessing ROI selection SEM terminal Trak TrakEM2 ultramicrotomy

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